Kaito Yashio and his friend Akiho Senomiya are the remaining members of their school's Robotics Club. After Akiho hands in a budget request to the staff room, both she and Kaito, who spends his time playing games on his PokeCon device, visit an old hangar containing a large robot the Robotics Club has been working on since its foundation, Gunvarrel, based on a popular robot anime whose final episode was never aired. The next day, the vice-principal agrees to give the Robotics Club their proposed budget on the condition that they win a robot tournament taking place in two week's time, with the club to be disbanded should they lose. As Kaito and Akiho contemplate if they can pull off such a feat, a mysterious girl is seen making a report.

Needing a robot for the tournament, Kaito and Akiho find an old Tanegashi Machine hobby robot in storage, only to find its batteries have run out. Akiho goes to see an old man named Tetsuharu 'Doc' Fujita to try and get some new parts, but finds they are too expensive. Kaito asks shopkeeper Mizuka Irei to look into any weaknesses Doc may have so he can lower his prices. This leads Akiho to meet Doc's granddaughter, Junna Daitoku. Although Junna fails to be much help, Akiho manages to get the parts needed thanks to an advanced allowance and a promise that they'll pay with the prize money. After repairing the robot, Akiho and Kaito work on controlling it, with Kaito also having to deal with Akiho's 'elephant mouse syndrome', an ailment she got following an accident seven years ago in which time fasts forward for her. Noticing her fatigue, Kaito agrees to be the robot's operator on the condition that she makes the controls similar to his favourite game, Kill Ballad.

Kaito and Akiho go with their teacher, Mitsuhiko Nagafukada, to where the Robo-One tournament is being held, though they have no hotel to check into. As Kaito practises with the robot, he experiences a strange sensation for a brief moment. The tournament soon begins and Kaito manages to use his tactics to get through the preliminaries and into the finals. Before the final match, Akiho starts to grow concerned about Kaito, who hadn't gotten a lot of sleep prior to the tournament. The final match soon begins against the reigning champion, Mr. Pleiades, whose robot has some fierce tricks up its sleeve. While Kaito's robot is at a disadvantage against Subaru's, Kaito suddenly experiences an inverse of the ailment Akiho has, slowing down time for him, and makes a counterattack, knocking both of them out, though this technically results in Kaito's loss. Upon returning home, Kaito has a brief encounter with Kill Ballad's creator, Frau Koujirou.

Akiho tries to get her father, who is the president of the Tanegashima Space Center, to fund their giant robot project, but her mother soon quenches that line of thought. Later, Kaito is called to meet with Frau Koujiro, whose real name is Kona Furugoori, to help her move into her dorm as she is transferring into his school. Following more intel from Mizuka, Akiho goes to see Mitsuhiko's uncle, who runs a candy factory, to request sponsorship for their robot. Meanwhile, Subaru manages to get Kaito's assistance for an upcoming Robo-1 tournament in Las Vegas. As Subaru questions about what Kaito did during the tournament, Kaito recalls an incident on September 11, 2010, in which he and Akiho were part of a mass fainting aboard a ferry, where they both contracted elephant mouse syndrome. Later that night, Kaito hears a strange voice coming from his PokeCon.

Becoming curious about the girl she saw the other day, Kaito hears from Junna about various sightings of the girl. As Akiho and Subaru deal with an interview for the Robo-One tournament, Kaito and Junna go to the beach, where they encounter the cadaver of a beached whale. Hearing that Junna has retired from the karate club, Kaito suggests she pay a visit to the Robotics Club. Later that night, Kaito hears the strange voice again, leading him to an abandoned room in school, where he finally encounters the girl through his PokeCon. This AI, named Airi, reveals herself to be an Iru-O app that had attempted to contact Kaito over the past 8 years. She then shows Kaito a hidden file, containing a log by one Kou Kimijima, predicting gigantic solar flares would occur on certain years. As Kaito ponders how many of those predictions turned out to be accurate, Mizuka has a strange reaction where she hears Kaito mention Kimijima's name.

Kaito arrives before Misaki, with the others helping to divert the missiles she fires using AR decoys, although Kaito is forced to use the Slow-Mo and sacrifice one of his pile bunkers to dodge the last one. Kaito manages to get up close to Misaki's Sumeragi and use the Slow-Mo to attack her with the other pile bunker. However, this knocks Misaki out and allows Kimijima to take full control of her as he divides the Sumeragi into a more mobile unit. After locking down the launch sequence, despite Nao and the other adults reclaming the control room, Kimijima launches an attack at the others forcing them to seperate, which leaves the Super Gunbuild-1 with only five minutes of power. Just then, Kona receives a program from Sawada that will erase Kimijima if they can get his avatar in the PokeCom's view, although it requires a reboot which leaves Kaito vulnerable.